TABLE 4.

Five commonly employed core methods along with descriptions and the number of publications using them found within Web of Science, accessed April 2018^a

Core method	Description	No. of publications
Abundance-based	Accounts for read depth (a portion of the top 75% of total reads); abundance	6
Occupancy-based	Accounts for sample size (present in >50% of samples); occupancy	24
Abundance and occupancy-based	Accounts for both sample size and read depth (present in >50% of samples with minimum abundance >0.02% of total reads); abundance and occupancy	3
Hard cutoffs of abundance and occupancy	Uses a specific no. of samples or reads (present in 5 samples with 25 total reads); abundance and occupancy	4
Venn diagram (e.g., stringent occupancy)a	Present in all subsets of samples	8

^aThe Venn diagram method was not utilized in our analysis due to its similarity to the proportion of replicates method.